Managing self-pollinated germplasm collections to maximize utilization

2011 ◽  
Vol 9 (01) ◽  
pp. 123-133 ◽  
Author(s):  
Randall L. Nelson
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Germplasm Collection ◽  
Whole Genome ◽  
Germplasm Collections ◽  
Seed Distribution ◽  
Future Potential ◽  
Primary Mission ◽  
Germplasm Accessions ◽  
Current Potential

The primary mission of germplasm collections is to preserve genetic diversity, but germplasm is preserved so that it can be used. Historically, the standard practice is that all germplasm accessions should be maintained as collected, so that even self-pollinated accessions are maintained as heterogeneous seed lots. In theory, this seems like an ideal strategy for preserving genetic diversity, but in practice, it is simply not workable. Heterogeneous accessions are in constant risk of change and loss. It is possible to mitigate the risk factors, but they can only be lessened and not eliminated. Maintaining pure-lined accessions for self-pollinated species not only eliminates the problems associated with genetic drift and natural selection, but also enhances the accuracy of the evaluations and fosters effective germplasm utilization. Neither the current potential to characterize entire germplasm collections with tens of thousands of DNA markers nor the future potential of whole genome sequencing to completely characterize the diversity of all accessions in collections can be fully realized for self-pollinated species unless accessions are homogeneous and homozygous. In this manuscript, the case is made for pure-lining self-pollinated germplasm accessions using the USDA Soybean Germplasm Collection, which has maintained pure-lined accessions for over 50 years, as an example. There is also an analysis of the extensive seed distribution from this collection to indicate the value of a diverse collection of genotypes.

scholarly journals Harnessing genetic diversity in the USDA pea (Pisum sativum L.) germplasm collection through genomic prediction

2021 ◽  
Author(s):  
Md Abdullah Al Bari ◽  
Ping Zheng ◽  
Indalecio Viera ◽  
Hannah Worral ◽  
Stephen Szwiec ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Seed Yield ◽  
Genomic Prediction ◽  
Prediction Models ◽  
Germplasm Collection ◽  
Predictive Ability ◽  
Germplasm Collections ◽  
Pisum Sativum L ◽  
Generation Sequencing ◽  
Germplasm Accessions

Phenotypic evaluation and efficient utilization of germplasm collections can be time-intensive, laborious, and expensive. However, with the plummeting costs of next-generation sequencing and the addition of genomic selection to the plant breeder's toolbox, we now can more efficiently tap the genetic diversity within large germplasm collections. In this study, we applied and evaluated genomic selection's potential to a set of 482 pea accessions, genotyped with 30,600 SNP markers and phenotyped for seed yield and yield-related components, for enhancing selection of accessions from the USDA Pea Germplasm Collection. Genomic prediction models and several factors affecting predictive ability were evaluated in a series of cross-validation schemes across complex traits. Different genomic prediction models gave similar results, with predictive ability across traits ranging from 0.23 to 0.60, with no model working best across all traits. Increasing the training population size improved the predictive ability of most traits, including seed yield. An increasing trend in predictive ability was also observed with an increasing number of SNPs. Accounting for population structure effects did not significantly boost predictive ability, but we observed a slight improvement in seed yield. By applying the genomic prediction model from this study, we then examined the distribution of nonphenotyped accessions, and the reliability of genomic estimated breeding values (GEBV) of the USDA Pea accessions genotyped but not phenotyped. The distribution of GEBV suggested that none of the nonphenotyped accessions were expected to perform outside the range of the phenotyped accessions. Desirable breeding values with higher reliability can be used to identify and screen favorable germplasm accessions. Expanding the training set and incorporating additional orthogonal information into the genomic prediction framework could enhance prediction accuracy. Keywords: genomic selection, genomic prediction, reliability criteria, germplasm accessions, pea (Pisum sativum L.), next-generation sequencing

Ecogeographical studies identify diversity and potential gaps in the largest germplasm collection of bladder clover (Trifolium spumosum L.)

2007 ◽  
Vol 58 (7) ◽  
pp. 728 ◽  
Author(s):  
K. Ghamkhar ◽  
R. Snowball ◽  
S. J. Bennett
Keyword(s):  
Genetic Diversity ◽  
Germplasm Collection ◽  
Principal Component ◽  
Collection Site ◽  
Plant Germplasm ◽  
Germplasm Collections ◽  
Ecological Aspects ◽  
Passport Data ◽  
Ecogeographical Diversity ◽  
Germplasm Accessions

Plant germplasm collections are important reservoirs of diversity for plant breeders and adding to the knowledge of the diversity among and within germplasm accessions helps plant breeders to use them more efficiently. The annual legume, bladder clover (Trifolium spumosum L.), was the model plant in this study. The hypothesis that ecogeographical variables are important sources of diversity in the germplasm collection of bladder clover and some variables are more important than others has been studied. Three themes have been addressed here: firstly, analysis of the existing passport data to determine a minimum set of ecogeographical descriptors required for capturing ecological aspects of each collection site; secondly, illustration of the ecogeographical regions and subregions using GIS techniques to identify areas with the greatest likelihood of filling gaps in the collection; thirdly, development of an approach for the evaluation of genetic diversity by grouping accessions with a focus on outliers within the collection using principal component and cluster analyses. In this paper the importance of longitude as a geographical factor has been documented and the overall ecogeographical diversity in the germplasm collection of bladder clover has been screened.

scholarly journals Harnessing Genetic Diversity in the USDA Pea Germplasm Collection Through Genomic Prediction

2021 ◽  
Vol 12 ◽  
Author(s):  
Md. Abdullah Al Bari ◽  
Ping Zheng ◽  
Indalecio Viera ◽  
Hannah Worral ◽  
Stephen Szwiec ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Seed Yield ◽  
Genomic Prediction ◽  
Complex Traits ◽  
Prediction Models ◽  
Germplasm Collection ◽  
Predictive Ability ◽  
Snp Markers ◽  
Breeding Values ◽  
Germplasm Collections

Phenotypic evaluation and efficient utilization of germplasm collections can be time-intensive, laborious, and expensive. However, with the plummeting costs of next-generation sequencing and the addition of genomic selection to the plant breeder’s toolbox, we now can more efficiently tap the genetic diversity within large germplasm collections. In this study, we applied and evaluated genomic prediction’s potential to a set of 482 pea (Pisum sativum L.) accessions—genotyped with 30,600 single nucleotide polymorphic (SNP) markers and phenotyped for seed yield and yield-related components—for enhancing selection of accessions from the USDA Pea Germplasm Collection. Genomic prediction models and several factors affecting predictive ability were evaluated in a series of cross-validation schemes across complex traits. Different genomic prediction models gave similar results, with predictive ability across traits ranging from 0.23 to 0.60, with no model working best across all traits. Increasing the training population size improved the predictive ability of most traits, including seed yield. Predictive abilities increased and reached a plateau with increasing number of markers presumably due to extensive linkage disequilibrium in the pea genome. Accounting for population structure effects did not significantly boost predictive ability, but we observed a slight improvement in seed yield. By applying the best genomic prediction model (e.g., RR-BLUP), we then examined the distribution of genotyped but nonphenotyped accessions and the reliability of genomic estimated breeding values (GEBV). The distribution of GEBV suggested that none of the nonphenotyped accessions were expected to perform outside the range of the phenotyped accessions. Desirable breeding values with higher reliability can be used to identify and screen favorable germplasm accessions. Expanding the training set and incorporating additional orthogonal information (e.g., transcriptomics, metabolomics, physiological traits, etc.) into the genomic prediction framework can enhance prediction accuracy.

Correction of the misclassification of species in the Portuguese collection of Cucurbita pepo L. using DNA markers

2014 ◽  
Vol 12 (S1) ◽  
pp. S160-S163 ◽  
Author(s):  
Ricardo Rodrigues ◽  
Iris Veiga ◽  
António Marreiros ◽  
Filomena Rocha ◽  
José Leitão
Keyword(s):  
Dna Markers ◽  
Cucurbita Pepo ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Germplasm Collection ◽  
Phenotypic Analysis ◽  
Germplasm Collections ◽  
Molecular Patterns ◽  
Rapd And Issr ◽  
Single Sequence

In this study, the genetic variability among 130 accessions of the Portuguese germplasm collection of Cucurbita pepo L. maintained at the Banco Português de Germoplasma Vegetal was assessed using AFLP (amplified fragment length polymorphism) and RAPD (random amplified polymorphic DNA) techniques for the identification of a genetically diverse core group of accessions for field phenotypic analysis. The surprisingly completely different molecular patterns exhibited by multiple accessions was later confirmed in the distribution of the putative C. pepo plants into two clusters drastically separated at a very low level of genetic similarity (DICE coefficient = 0.37). Additional analyses with RAPD and ISSR (inter single sequence repeat) markers and the introduction of standard genotypes of C. maxima L. and C. moschata L. into the analyses allowed the identification of multiple accessions of the last species wrongly included in the C. pepo collection. This study is a good example of the usefulness of DNA markers in the establishment and management of plant germplasm collections.

scholarly journals Genetic diversity of Cuban pineapple germplasm assessed by AFLP Markers

2012 ◽  
Vol 12 (2) ◽  
pp. 104-110 ◽  
Author(s):  
Ermis Yanes Paz ◽  
Katia Gil ◽  
Laureano Rebolledo ◽  
Andrés Rebolledo ◽  
Daniel Uriza ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Morphological Characterization ◽  
Aflp Markers ◽  
Ananas Comosus ◽  
Morphological Descriptors ◽  
Low Level ◽  
Germplasm Collections

The Cuban pineapple germplasm collection represents the genetic diversity of pineapple cultivated in that country and includes other important genotypes obtained from the germplasm collections in Brazil and Martinique. The collection has previously been characterized with morphological descriptors but a molecular characterization has been lacking. With this aim, 56 six genotypes of A. comosus and one of Bromelia pinguin were analyzed with a total of 191 AFLP markers. A dendrogram that represents the genetic relationships between these samples based on the AFLP results showed a low level of diversity in the Cuban pineapple collection. All Ananas comosus accessions, being the majority obtained from farmers in different regions in Cuba, are grouped at distances lower than 0.20. Molecular characterization was in line with morphological characterization. These results are useful for breeding and conservation purposes.

Genetic diversity of Dioscorea japonica germplasm in Taiwan revealed by inter-simple sequence repeat DNA markers

2015 ◽  
Vol 14 (3) ◽  
pp. 211-218
Author(s):  
Tsai-Li Kung ◽  
Kuan-Hung Lin ◽  
Shun-Fu Lin
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Dna Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Inter Simple Sequence Repeat ◽  
Northern Region ◽  
Sequence Repeat ◽  
Dioscorea Japonica ◽  
Simple Sequence

There are three native varieties of edible yams (Dioscorea japonica Thunb.) in Taiwan, but germplasm has been collected from only a few. To assess the genetic diversity of 99 accessions collected from four geographically diverse regions, inter-simple sequence repeat (ISSR) DNA markers were analysed, and 90.2% of the polymorphic markers in these accessions were found. Genetic similarity among accessions ranged from 30.8 to 74.4%, averaging 48.4%. Cluster analyses revealed four main clusters plus one outlier (Dioscorea alata L.). The varieties oldhamii and pseudojaponica were separated into different clusters and var. japonica was grouped with both varieties. Since var. japonica was found to be genetically similar to var. oldhamii and var. pseudojaponica, we suggest that var. japonica is a hybrid or intermediate variety between the two varieties. Molecular analysis of variance results indicated that variation within counties (95.94%) was predominantly greater than variation among counties (3.63%) and among regions (0.43%). Overall, gene flow (Nm= 0.970) estimated from genetic differentiation (Gst= 0.340) suggests that gene flow among regions is relatively high. The highest genetic diversity (H= 0.191) and Shannon's index (I= 0.312), and a high gene flow (Nm= 3.926) of germplasm in the northern region suggest that this region is a possible centre of dispersal and domestication of yams in Taiwan. This study provided valuable information for germplasm collection and genetic improvement.

scholarly journals A perfect storm: ploidy and preadaptation facilitate Saccharum spontaneum escape and invasion in the Republic of Panama

2020 ◽  
Author(s):  
Kristin Saltonstall ◽  
Graham D. Bonnett ◽  
Karen S. Aitken
Keyword(s):  
Genetic Diversity ◽  
Perennial Grass ◽  
Germplasm Collection ◽  
High Survival ◽  
Saccharum Spontaneum ◽  
Local Conditions ◽  
Ploidy Levels ◽  
Germplasm Collections ◽  
High Ploidy ◽  
Sugarcane Germplasm

AbstractPolyploidy may contribute to invasive ability as it can lead to high survival and fitness during establishment and enhance the processes of adaptation to novel environments by increasing genetic diversity in invading propagules. Many grasses are polyploid and many are aggressive invaders, making them persistent problems in disturbed environments worldwide. Today, vast areas of central Panama are dominated by Saccharum spontaneum, a perennial grass that originates from Asia. While widely regarded as invasive, it is not known when or how it arrived in Panama. We explore hypotheses regarding the timing and origins of this invasion through literature review and comparisons of genetic diversity in Panama with accessions from available sugarcane germplasm collections, highlighting historical accessions that were likely brought to Panama in 1939 as part of a USDA sugarcane germplasm collection. Samples were haplotyped at two chloroplast loci and genotyped using eight microsatellite markers. All sequenced individuals from Panama belong to a single chloroplast lineage which is common worldwide and was common in the Historic germplasm collection. Although genotypic diversity was extremely high in all samples due to high ploidy, samples from Panama had reduced diversity and clustered with several accessions in the Historic collection which had the same haplotype and high ploidy levels. Our results suggest that accidental escape from the historical sugarcane germplasm collection is the likely origin of the S. spontaneum invasion in Panama. Intraspecific hybridization among several historical accessions and pre-adaptation to local conditions may have facilitated its rapid spread and persistence. We discuss the implications of our findings for biosecurity of germplasm collections.

Genetic diversity within Lablab purpureus and the application of gene-specific markers from a range of legume species

2007 ◽  
Vol 5 (03) ◽  
pp. 154-171 ◽  
Author(s):  
S. C. Venkatesha ◽  
M. Byre Gowda ◽  
P. Mahadevu ◽  
A. Mohan Rao ◽  
D.-J. Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Expressed Sequence Tag ◽  
Rapd Marker ◽  
Germplasm Collection ◽  
Lablab Purpureus ◽  
Specific Primer ◽  
Southern States ◽  
Germplasm Collections ◽  
Marker Study

Molecular markers have been used to study genetic diversity within a set ofLablabpurpureusaccessions collected from the southern states of India. Amplified fragment length polymorphism (AFLP) molecular marker studies using a total of 78L.purpureusaccessions with nine primer combinations showed there was very little genetic diversity within theL.purpureusaccessions from the southern Indian germplasm collection as compared to a set of 15 accessions from other international germplasm collections that included African accessions. The set of 15 were selected from a random amplified length polymorphism (RAPD) marker study and chosen on the basis of widest genetic distance. Further molecular analysis with polymerase chain reaction (PCR) markers from 97 expressed sequence tag (EST) and gene-specific primer pairs, designed from a range of legume sequences, concurred with the AFLP analyses. Both of these approaches provide a wealth of markers for diversity and mapping studies. The 97 sequence-specific primer pairs tested inL.purpureusresulted in 70% amplification success, with 44% of primer pairs amplifying single bands and 10% double bands. Markers generated from these EST and genomic sequences provide useful cross-reference to comparative legume genomics that will potentially have long-term benefit to legume plant breeding.

Study of genetic diversity in wild raspberry (Rubus idaeus L.) germplasm collection using morphological characters and RAPD markers

Biologija ◽  
2008 ◽  
Vol 54 (2) ◽  
pp. 66-74 ◽  
Author(s):  
Jolanta Patamsytė ◽  
Donatas Žvingila ◽  
Juozas Labokas ◽  
Virgilijus Baliuckas ◽  
Laimutė Balčiūnienė ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Germplasm Collection ◽  
Morphological Characters ◽  
Rubus Idaeus

ANALYSIS OF GENETIC STRUCTURE OF DOGS OF FRENCH BULLDOG BREED USING MICROSATELLITE DNA MARKERS

2018 ◽  
Vol 51 ◽  
pp. 185-192
Author(s):  
S. Kruhlyk ◽  
V. Dzitsiuk ◽  
V. Spyrydonov
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Dna Markers ◽  
Microsatellite Dna ◽  
High Variability ◽  
Molecular Diagnostic ◽  
Allelic Variants ◽  
Microsatellite Dna Markers ◽  
Gene Complexes ◽  
French Bulldog

Genetic variability of domestic dogs is a source for effective process of breed formation and creating unique gene complexes. In the world, for preservation of genetic resources of dogs, there are dog training associations which have great confidence: American Club Dog Breeders (AKC), the British Kennel Club (KC) and the Federation Cynologique Internationale (FCI), aimed at protecting breeding dogs, standards creation, registration of a breed, and issuance of accurate pedigrees. Evaluation of the genetic diversity of dog breeds is able to significantly complement and improve their breeding programs. Since breeds of dog differ in morphological and economic characteristics, the problem of finding of the breed features in the genome of animals is becoming more topical. From this point of view, French Bulldog is an interesting breed of dog (FRANC.BULLDOGGE, FCI standard number 101) which belongs by the classification of breeds, adopted in FCI, to the group IX – a dog-companion for health and fun, but to a subgroup of fighting dogs of a small format. French Bulldog breed has been researched slightly not only in Ukraine and also abroad, as the main work of all dog association is focused on solving theoretical and practical issues of breeding, keeping, feeding, veterinary protection and others. The study was conducted at Research Department of Molecular Diagnostic Tests of Ukrainian Laboratory of Quality and Safety of Agricultural Products. 33 animals of French Bulldog breed, admitted to use in dog breeding of Ukrainian Kennel Union (UKU), were involved for the genetic analysis using DNA markers. The materials of the research were buccal epithelial cells, selected before the morning feeding of animals by scraping mucous membrane of oral cavity with disposable, dry, sterile cotton swab. Genomic DNA was extracted using KIT-set of reagents for DNA isolation according to the manufacturer's instructions. PEZ1, PEZ3, PEZ6, PEZ8, FHC 2010, FHC 2054 markers, recommended by International Society for Animal Genetics (ISAG), ACN, КC and FCI, were used for research. As a result of research 25 alleles for all the loci were detected in the experimental sample of dogs. The average number of alleles at the locus Na, obtained by direct counting, was 4.16. The most polymorphic loci for this breed were PEZ6 and PEZ3 with 8 and 6 allelic variants. Monomorphic loci were PEZ8 and FHC 2054 which had 4 and 3 alleles and the lowest level of polymorphism was observed for PEZ 1 and FHC 2010 loci in which only 2 alleles were identified. On analyzing the molecular genetic characteristics of dogs of French Bulldog breed, we found a high variability of genotype on rare alleles, which included alleles: M, C, D, E, J, K, L, O, N and representing 60% of the total number of the identified alleles. C, D, E alleles for PEZ3 locus and O allele at PEZ6 locus are unique to the sampling of dogs because they are not repeated in other loci. Typical alleles: N, F, R, I, P, K, M are 40% of the total. But F, R alleles for PEZ3 locus and P allele for locus PEZ6 are not repeated either in standard allelic variants or in rare one, indicating a high information content of these alleles and loci to be used for further monitoring of allele pool, genetic certification and identification of dogs. Microsatellite DNA loci were analyzed as a result of investigations of French Bulldogs and the most informative: PEZ3, PEZ6 and PEZ8 were found, which have high efficiency in individual and breed certification of dogs due to high variability. These data allow further monitoring of the state of genetic diversity of the breed and the development of measures for improvement of breeding to preserve the structure of breeding material. The study of individual and population genetic variability is advisable to continue for breeding of French Bulldogs "in purity" and preserving valuable gene complexes. The results are the basis for further monitoring of the proposed informative panels of microsatellite DNA markers for genotyping dog of French Bulldog breed and their complex evaluation.

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